From 6ca6c98980b8c642e06d43ab94e2b2174f81c5cb Mon Sep 17 00:00:00 2001
From: chartl <chartl@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 3 Mar 2010 16:50:58 +0000
Subject: [PATCH] Can just give PickSequenomProbes a dbsnp rod to mask

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2920 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/fasta/PickSequenomProbes.java   | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/PickSequenomProbes.java b/java/src/org/broadinstitute/sting/gatk/walkers/fasta/PickSequenomProbes.java
index 0f08239ff..57de80817 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/PickSequenomProbes.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/fasta/PickSequenomProbes.java
@@ -33,9 +33,13 @@ public class PickSequenomProbes extends RefWalker<String, String> {
     public void initialize() {
 		if ( SNP_MASK != null ) {
             logger.info("Loading SNP mask...  ");
-            ReferenceOrderedData<TabularROD> snp_mask = new ReferenceOrderedData<TabularROD>("snp_mask",
-                    new java.io.File(SNP_MASK), TabularROD.class);
-
+            ReferenceOrderedData snp_mask;
+            if ( SNP_MASK.contains("dbsnp")) {
+                snp_mask = new ReferenceOrderedData<rodDbSNP>("snp_mask",new java.io.File(SNP_MASK),rodDbSNP.class);
+            } else {
+                snp_mask = new ReferenceOrderedData<TabularROD>("snp_mask",
+                        new java.io.File(SNP_MASK), TabularROD.class);
+            }
             snpMaskIterator = snp_mask.iterator();
 		}
     }